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maccallumlab / meld

Modeling with limited data
http://meldmd.org
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Add density map restraints support #139

Closed ccccclw closed 1 year ago

ccccclw commented 1 year ago

Hi Justin, I updated the implementation of density map restraints. The map potentials for each replica are calculated before simulation given "blur" scaler. Currently, it doesn't use the replica ladder adaptation by changing alpha values, as exchanges are usually fine and this can save the time for recalculation of map potential. High dimensional maps slow down simulations, which I think is caused by sending the map potential data to gpu at each exchange step. Do you have any suggestions for this considering the map potential for each replica is fixed during simulation?

jlmaccal commented 1 year ago

I'm having a hard time merging this into master.

Can you please:

  1. Merge the master branch into your density branch.
  2. Eliminate all of the merge conflicts.
  3. Eliminate any TODO items in the code that are no longer relevant
  4. Make sure that the test suite passes.
  5. Submit a new pull request.

If you can do that, I'll merge as soon as possible.

jlmaccal commented 1 year ago

I should also add to do the PR against master.